Have a look at this page:
http://support.google.com/a/bin/answer.py?answer=96917
Click on the first radio button ("I'm receiving the message 'This domain is already in use.'")
Toward the bottom of the page, there will be a URL template:
https://www.google.com/a/cpanel/<your domain name>/VerifyAdminAccountPasswordReset
Sign into your Google Apps account, then substitute your domain name in the above URL-template where indicated.
When you visit the resulting URL, Google will ask you for an email address. You will then get an email supplying data values for a new CNAME record you can add at your domain-registrar's website. If you do that correctly, Google will then consider your custom domain as verified.